8cw2

From Proteopedia

(Difference between revisions)

Revision as of 20:30, 12 April 2023

Crystal structure of TDP1 complexed with compound XZ760

Structural highlights

8cw2 is a 2 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

TYDP1_HUMAN Defects in TDP1 are the cause of spinocerebellar ataxia autosomal recessive with axonal neuropathy (SCAN1) [MIM:607250. SCAN1 is an autosomal recessive cerebellar ataxia (ARCA) associated with peripheral axonal motor and sensory neuropathy, distal muscular atrophy, pes cavus and steppage gait as seen in Charcot-Marie-Tooth neuropathy. All affected individuals have normal intelligence.^[1] ^[2] ^[3] ^[4] ^[5]

Function

TYDP1_HUMAN DNA repair enzyme that can remove a variety of covalent adducts from DNA through hydrolysis of a 3'-phosphodiester bond, giving rise to DNA with a free 3' phosphate. Catalyzes the hydrolysis of dead-end complexes between DNA and the topoisomerase I active site tyrosine residue. Hydrolyzes 3'-phosphoglycolates on protruding 3' ends on DNA double-strand breaks due to DNA damage by radiation and free radicals. Acts on blunt-ended double-strand DNA breaks and on single-stranded DNA. Has low 3'exonuclease activity and can remove a single nucleoside from the 3'end of DNA and RNA molecules with 3'hydroxyl groups. Has no exonuclease activity towards DNA or RNA with a 3'phosphate.^[6] ^[7] ^[8] ^[9] ^[10]

References

↑ Interthal H, Chen HJ, Champoux JJ. Human Tdp1 cleaves a broad spectrum of substrates, including phosphoamide linkages. J Biol Chem. 2005 Oct 28;280(43):36518-28. Epub 2005 Aug 31. PMID:16141202 doi:M508898200
↑ Zhou T, Lee JW, Tatavarthi H, Lupski JR, Valerie K, Povirk LF. Deficiency in 3'-phosphoglycolate processing in human cells with a hereditary mutation in tyrosyl-DNA phosphodiesterase (TDP1). Nucleic Acids Res. 2005 Jan 12;33(1):289-97. Print 2005. PMID:15647511 doi:33/1/289
↑ Takashima H, Boerkoel CF, John J, Saifi GM, Salih MA, Armstrong D, Mao Y, Quiocho FA, Roa BB, Nakagawa M, Stockton DW, Lupski JR. Mutation of TDP1, encoding a topoisomerase I-dependent DNA damage repair enzyme, in spinocerebellar ataxia with axonal neuropathy. Nat Genet. 2002 Oct;32(2):267-72. Epub 2002 Sep 16. PMID:12244316 doi:10.1038/ng987
↑ Hirano R, Interthal H, Huang C, Nakamura T, Deguchi K, Choi K, Bhattacharjee MB, Arimura K, Umehara F, Izumo S, Northrop JL, Salih MA, Inoue K, Armstrong DL, Champoux JJ, Takashima H, Boerkoel CF. Spinocerebellar ataxia with axonal neuropathy: consequence of a Tdp1 recessive neomorphic mutation? EMBO J. 2007 Nov 14;26(22):4732-43. Epub 2007 Oct 18. PMID:17948061 doi:7601885
↑ Interthal H, Chen HJ, Kehl-Fie TE, Zotzmann J, Leppard JB, Champoux JJ. SCAN1 mutant Tdp1 accumulates the enzyme--DNA intermediate and causes camptothecin hypersensitivity. EMBO J. 2005 Jun 15;24(12):2224-33. Epub 2005 May 26. PMID:15920477 doi:7600694
↑ Inamdar KV, Pouliot JJ, Zhou T, Lees-Miller SP, Rasouli-Nia A, Povirk LF. Conversion of phosphoglycolate to phosphate termini on 3' overhangs of DNA double strand breaks by the human tyrosyl-DNA phosphodiesterase hTdp1. J Biol Chem. 2002 Jul 26;277(30):27162-8. Epub 2002 May 21. PMID:12023295 doi:10.1074/jbc.M204688200
↑ Raymond AC, Rideout MC, Staker B, Hjerrild K, Burgin AB Jr. Analysis of human tyrosyl-DNA phosphodiesterase I catalytic residues. J Mol Biol. 2004 May 14;338(5):895-906. PMID:15111055 doi:10.1016/j.jmb.2004.03.013
↑ Raymond AC, Staker BL, Burgin AB Jr. Substrate specificity of tyrosyl-DNA phosphodiesterase I (Tdp1). J Biol Chem. 2005 Jun 10;280(23):22029-35. Epub 2005 Apr 4. PMID:15811850 doi:M502148200
↑ Interthal H, Chen HJ, Champoux JJ. Human Tdp1 cleaves a broad spectrum of substrates, including phosphoamide linkages. J Biol Chem. 2005 Oct 28;280(43):36518-28. Epub 2005 Aug 31. PMID:16141202 doi:M508898200
↑ Gao R, Huang SY, Marchand C, Pommier Y. Biochemical characterization of human tyrosyl-DNA phosphodiesterase 2 (TDP2/TTRAP): a Mg(2+)/Mn(2+)-dependent phosphodiesterase specific for the repair of topoisomerase cleavage complexes. J Biol Chem. 2012 Aug 31;287(36):30842-52. doi: 10.1074/jbc.M112.393983. Epub, 2012 Jul 20. PMID:22822062 doi:10.1074/jbc.M112.393983

1 Structural highlights
2 Disease
3 Function
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/8cw2"

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 8cw2 is ON HOLD  until Paper Publication
+==Crystal structure of TDP1 complexed with compound XZ760==
+<StructureSection load='8cw2' size='340' side='right'caption='[[8cw2]], [[Resolution|resolution]] 1.81&Aring;' scene=''>
-Authors: Lountos, G.T., Zhao, X.Z., Wang, W., Kiselev, E., Tropea, J.E., Needle, D., Pommier, Y., Burke, T.R.
+== Structural highlights ==
+<table><tr><td colspan='2'>[[8cw2]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8CW2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8CW2 FirstGlance]. <br>
-Description: Crystal structure of TDP1 complexed with compound XZ760
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MPO:3[N-MORPHOLINO]PROPANE+SULFONIC+ACID'>MPO</scene>, <scene name='pdbligand=OYR:4-({(4R)-7-phenyl-2-[4-(2-{[4-(pyridin-2-yl)phenyl]methoxy}ethyl)phenyl]imidazo[1,2-a]pyridin-3-yl}amino)benzene-1,2-dicarboxylic+acid'>OYR</scene></td></tr>
-[[Category: Unreleased Structures]]
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=8cw2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8cw2 OCA], [https://pdbe.org/8cw2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8cw2 RCSB], [https://www.ebi.ac.uk/pdbsum/8cw2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8cw2 ProSAT]</span></td></tr>
-[[Category: Wang, W]]
+</table>
-[[Category: Lountos, G.T]]
+== Disease ==
-[[Category: Burke, T.R]]
+[https://www.uniprot.org/uniprot/TYDP1_HUMAN TYDP1_HUMAN] Defects in TDP1 are the cause of spinocerebellar ataxia autosomal recessive with axonal neuropathy (SCAN1) [MIM:[https://omim.org/entry/607250 607250]. SCAN1 is an autosomal recessive cerebellar ataxia (ARCA) associated with peripheral axonal motor and sensory neuropathy, distal muscular atrophy, pes cavus and steppage gait as seen in Charcot-Marie-Tooth neuropathy. All affected individuals have normal intelligence.<ref>PMID:16141202</ref> <ref>PMID:15647511</ref> <ref>PMID:12244316</ref> <ref>PMID:17948061</ref> <ref>PMID:15920477</ref>
-[[Category: Pommier, Y]]
+== Function ==
-[[Category: Kiselev, E]]
+[https://www.uniprot.org/uniprot/TYDP1_HUMAN TYDP1_HUMAN] DNA repair enzyme that can remove a variety of covalent adducts from DNA through hydrolysis of a 3'-phosphodiester bond, giving rise to DNA with a free 3' phosphate. Catalyzes the hydrolysis of dead-end complexes between DNA and the topoisomerase I active site tyrosine residue. Hydrolyzes 3'-phosphoglycolates on protruding 3' ends on DNA double-strand breaks due to DNA damage by radiation and free radicals. Acts on blunt-ended double-strand DNA breaks and on single-stranded DNA. Has low 3'exonuclease activity and can remove a single nucleoside from the 3'end of DNA and RNA molecules with 3'hydroxyl groups. Has no exonuclease activity towards DNA or RNA with a 3'phosphate.<ref>PMID:12023295</ref> <ref>PMID:15111055</ref> <ref>PMID:15811850</ref> <ref>PMID:16141202</ref> <ref>PMID:22822062</ref>
-[[Category: Zhao, X.Z]]
+== References ==
-[[Category: Tropea, J.E]]
+<references/>
-[[Category: Needle, D]]
+__TOC__
+</StructureSection>
+[[Category: Homo sapiens]]
+[[Category: Large Structures]]
+[[Category: Burke TR]]
+[[Category: Kiselev E]]
+[[Category: Lountos GT]]
+[[Category: Needle D]]
+[[Category: Pommier Y]]
+[[Category: Tropea JE]]
+[[Category: Wang W]]
+[[Category: Zhao XZ]]

8cw2

From Proteopedia

Revision as of 20:30, 12 April 2023

Crystal structure of TDP1 complexed with compound XZ760

Structural highlights

Disease

Function

References

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Proteopedia Page Contributors and Editors (what is this?)

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